Abstract Background To obviate malaria and other healthcare costs and enhance healthcare utilization, the government of Ghana introduced the National Health Insurance Scheme (NHIS) in 2005. Nonetheless, there is dearth of empirical evidence on Ghanaian women’s knowledge about whether malaria treatment is covered by the NHIS or not. The current study, therefore, investigated factors associated with knowledge of malaria treatment with the NHIS among women aged 15-49 in Ghana. Methods The study is a secondary analysis of data from women respondents in the 2014 Ghana Demographic and Health Survey. A total of 2,560 women participated in this study. Descriptive computation of the weighted proportion of women who knew that malaria is covered by NHIS was conducted at 95% confidence interval (CI). A multilevel logistic regression analyses was carried out with Stata’s MLwinN package version 3.05. We declared significance at 5% alpha. Findings from the models were reported as adjusted odds ratios (aOR) and credible intervals (CrIs). Results In all, 81.0% of Ghanaian women included in the study knew that NHIS covers malaria treatment. Women aged 45-49 had higher odds of knowing that NHIS covers malaria relative to those aged 15-19 age category [aOR=1.5;95%crl=1.2-2.1]. Women with higher education (post-secondary) had higher odds of knowing that NHIS covers malaria treatment compared with women who had no formal education [aOR=1.6;95%Crl=1.2-2.0]. Richest women were more likely to know that NHIS covers malaria treatment compared to the poorest women [aOR=1.3;95%Crl=1.2-1.7]. Women who had subscribed to the NHIS were more likely to report that NHIS covers malaria treatment [aOR=1.5;95%Crl=1.2-1.8]. The study revealed that the variance in the tendency for a woman to be aware that NHIS covers malaria treatment is attributable to 10.8% community level factors. Conclusion This study has shown that individual, community and regional level factors affect women’s knowledge on whether NHIS covers malaria treatment or not. As knowledge that malaria treatment is covered by NHIS may increase use of malaria prevention and treatment services in health facilities, we recommend that the Ghana Health Service intensifies community level education and awareness creation efforts, targeted at women among whom awareness levels are currently low.